When Nijô castle became property of the Imperial institution once again following the fall of the Tokugawa shogunate, the Tokugawa clan crests were predictably replaced with Imperial crests. However, as was apparently unknown or forgotten for about 150 years and only very recently (re)discovered, on the castle's karamon (Chinese-style gate) at least, the Tokugawa crests were not destroyed, but were left totally intact and were simply covered over.

The RocketNews article suggests a few possible reasons for this, including the intriguing idea of a symbolism of Imperial superiority, though now that I think about it, it could just as easily symbolize that this was and would always be a Tokugawa site, and/or symbolizing that the Tokugawa could never be destroyed but would always remain. On a practical level, too, I imagine the possibility that, perhaps, when this was done, it was not yet clear how permanent the Meiji Restoration would be. After all, the Kemmu Restoration only lasted a few years... so, practically speaking, maybe the carpenters thought it would be easier, or better, to leave the Tokugawa crests there, intact, underneath, in case this whole Imperial Restoration thing fell apart, and they needed to remove the Imperial crests.

Of course, there may be more logical/reasonable or more historically/contextually likely possibilities, but I'm just throwing out ideas.

This is something you see quite a lot of. For example, while everyone seems to think the walls/moats at Osaka Castle are the original Toyotomi walls, they're actually walls built by the Tokugawa directly on top of the Toyotomi walls (excavated Toyotomi walls were stacked rocks while the Tokugawa walls were fitted rock). There are spots on Himeji castle's roof tiles where the kamon were covered by that of a new lord when he took over the castle. You'd also see castles built on the foundations of old castles and reusing timber/tiles/etc from them.

There could be some element of the new boss making his mark and symbolically 'blotting out' their old foes (especially with the Tokugawa at Osaka, and less so the Emperor at Nijo...not to mention taking Edo Castle for the new Emperor's Palace). I don't think the Meiji government would have done it to show it would always be a Tokugawa site-they were pretty fanatic about discrediting and eliminating anything to do with the Tokugawa. I'd tend to think that in most cases it was done simply because it was the fastest and most economically feasible way. Totally removing and replacing the Tokugawa crests in the Nijo gate would have involved a LOT of work at a LOT of expense. Financially, the Meiji government started out extremely strapped for funds and would be so for decades. For Nijo, a castle that was basically unused by the Emperor and turned over to the city of Kyoto (a time when it was ransacked/vandalized by city officials over the years and allowed to fall into disrepair) the government wouldn't have wanted to sink any decent amount of money into it at first. The Tokugawa kamon weren't even covered until things got so bad in 1885 that the Imperial family reclaimed the castle and had to shell out to repair the damage-it being a rather expensive project, from all accounts the work was done hastily and on the cheap. Since this was 18 or so years into Meiji, it doesn't seem like it would have done to hedge against a 'failed experiment' in Imperial power as all the samurai rebellions and growing pains were things of the past.

There are other spots in Nijo castle where the Tokugawa crest seemingly never got covered/replaced by the Imperial-I remember asking about it on my first trip to Japan in 2000.